The suspect, identified only as 20-year-old Bilal C., is accused of having informed Abaaoud of ways to smuggle jihadists into Western Europe along the Balkans route then used by a mass influx of migrants.
He had also been in touch with Moroccan jihadist Ayoub El Khazzani, who opened fire with an assault rifle on an Amsterdam-Paris train last August but was overpowered by a group of Americans and a Briton, prosecutors said.
Bilal C. was already in custody "on another matter" when the German domestic intelligence service identified him as an IS suspect, said federal prosecutors in a statement. An investigating judge had issued a new arrest warrant.
The man allegedly travelled in 2014 from Algeria via Turkey to Syria where in December he joined Isis and received combat and weapons training.
In June 2015, Abaaoud allegedly instructed him "to explore the so-called Balkans route in terms of border controls and trafficking opportunities".
"As a result, the accused travelled from June to August 2015 from Syria via Turkey, Greece, Serbia and Hungary to Austria" before reaching Germany, the prosecutors said.
Along the way he had informed Abaaoud of "any open border crossings, waiting times, and arrival and departure routes," the statement said.
Several members of Isis that carried out the November 13 Paris attacks are suspected of having posed as refugees.
Abaaoud, a Belgian-Moroccan, was killed in November 2015 in a French police raid, aged 28.
Bilal C. had also kept Khazzani up to date on trafficking opportunities, "particularly from Turkey to Greece", the statement said.
Prosecutors said they had no evidence Bilal C. had been active on behalf of Isis since arriving in Germany.